Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV LETTER NEXT LETTER | FRAMES NO FRAMES

A B C D E F G H I K L M N O P Q R S T U V W X Y Z

## C

C - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
c1 - Variable in class org.metaqtl.Qtl
  The recombination rate between the QTL position and the left flanking marker.
c2 - Variable in class org.metaqtl.Qtl
  The recombination rate between the QTL position and the right flanking marker.
C_coeff - Static variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
canAddMoreQtl(double) - Method in class org.metaqtl.graph.QtlLayerBuffer
  Retruns true if more Qtl can be added to the configuration, false otherwise.
card - Variable in class org.metaqtl.TreeNode
  The number of sequences in the cluster
cartoFunction - Static variable in interface org.thalia.bio.entity.IGeneticMapProperties
cartoFunctionHaldane - Static variable in interface org.thalia.bio.entity.IGeneticMapProperties
cartoFunctionKey - Static variable in interface org.thalia.bio.entity.IGeneticMapProperties
cartoFunctionKosambi - Static variable in interface org.thalia.bio.entity.IGeneticMapProperties
ccov - Variable in class org.metaqtl.EMResult
  The complete information (just for means).
CENTROID_METHOD - Static variable in class org.metaqtl.algo.HClustAlgorithm
  Centroid method
CentroidMethod(double[], double[]) - Static method in class org.metaqtl.algo.HClustAlgorithm
  This method performs a hierarchical clustering of the given data points using a centroid method based on the mahalanobis distance.
cg - Variable in class org.metaqtl.Chromosome
  The number of generations of the offspring population.
checkProjection(ChromCluster[]) - Method in class org.metaqtl.algo.QtlProjAlgorithm
chi2 - Variable in class org.metaqtl.MetaChrom
  The chi-square value of this chromosome.
chi2 - Variable in class org.metaqtl.MultiFitResult
  The chi-square of the model.
children - Variable in class org.metaqtl.TreeNode
  Left and right children, or null
children - Variable in class org.thalia.bio.entity.bean.OntologyTermBean
  The children of the term.
CHISQUARE - Static variable in interface org.metaqtl.IBioLGroupProperties
  The key for the chisquare value.
chrom - Variable in class org.metaqtl.ChromCluster.ClusterEdge
CHROM_ALIGN_MODE - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_DISTANCE_SCALE - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_FLANKING_CEX - Static variable in class org.metaqtl.graph.MetaGraphPar
  The default cex parameter for flanking regions at the top and the end of the chromosome.
CHROM_NAME_FONT - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_NAME_HSPACE - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_STROKE - Static variable in class org.metaqtl.graph.MetaGraphPar
  The stroke of the chromosome shape.
CHROM_STROKE_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
  The color of the stroke of the Chromosome shape.
CHROM_TICK_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
  The color of the marker ticks on the chromosome.
CHROM_TICK_STROKE - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_TICK_WIDTH_1 - Static variable in class org.metaqtl.graph.MetaGraphPar
  The width of the marker ticks.
CHROM_TICK_WIDTH_2 - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_TICK_WIDTH_3 - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar
  The width of the chromosome.
ChromAxe - Class in org.metaqtl.graph
ChromAxe(double, double, double) - Constructor for class org.metaqtl.graph.ChromAxe
ChromCluster - Class in org.metaqtl
  A cluster of chromosomes which share the same name inside a `MapCluster` framwork.
ChromCluster() - Constructor for class org.metaqtl.ChromCluster
  Creates a new instance if ChromCluster.
ChromCluster.ClusterEdge - Class in org.metaqtl
ChromCluster.ClusterEdge(CMarkerSequence, Chromosome) - Constructor for class org.metaqtl.ChromCluster.ClusterEdge
ChromCluster.ClusterGraph - Class in org.metaqtl
ChromCluster.ClusterGraph(ChromCluster) - Constructor for class org.metaqtl.ChromCluster.ClusterGraph
ChromGraph - Class in org.metaqtl.graph
  A `ChromGraph` allows to link together a `Chromosome` and a `QtlPartition` in order to be depicted into a graphic.
ChromGraph() - Constructor for class org.metaqtl.graph.ChromGraph
ChromLayer - Class in org.metaqtl.graph
ChromLayer(double, double) - Constructor for class org.metaqtl.graph.ChromLayer
ChromLayer.CMrkTickPath - Class in org.metaqtl.graph
ChromLayer.CMrkTickPath() - Constructor for class org.metaqtl.graph.ChromLayer.CMrkTickPath
ChromLayer.CMrkTickPoint - Class in org.metaqtl.graph
ChromLayer.CMrkTickPoint() - Constructor for class org.metaqtl.graph.ChromLayer.CMrkTickPoint
chromNames - Variable in class org.metaqtl.MetaQtlAnalysis
  The names of the chromosomes.
chromNames - Variable in class org.metaqtl.MetaQtlModel
  The chromosomes.
Chromosome - Class in org.metaqtl
  On a Chromosome there are two types of locus : Marker QTL (Quantitative Trait Loci) inside a mapping context which is defined by both the mapping framework (function and unit) and the population cross design used to build this chromosome.
Chromosome() - Constructor for class org.metaqtl.Chromosome
chromosome - Variable in class org.metaqtl.graph.ChromGraph
  The chromosome to draw
ChromosomeAdapter - Class in org.metaqtl.adapter
  This class defines some usefull methods to adapt `Chromosome` objects into other kinds of objects or the inverse.
ChromosomeAdapter() - Constructor for class org.metaqtl.adapter.ChromosomeAdapter
chromosomes - Variable in class org.metaqtl.MetaMap
  The meta chromosomes.
ChromShape - Class in org.metaqtl.graph
ChromShape() - Constructor for class org.metaqtl.graph.ChromShape
ci - Variable in class org.metaqtl.Qtl
  The QTL confidence interval.
ci2sd(double) - Static method in class org.metaqtl.numrec.NumericalUtilities
ci_height - Variable in class org.metaqtl.graph.QtlShape
CI_MISS_IGNORE - Static variable in interface org.metaqtl.IMetaQtlConstants
  MSD Mode : ignore QTL with missing standard deviation.
CI_MISS_IMPUTATION - Static variable in interface org.metaqtl.IMetaQtlConstants
  MSD Mode : replace missing standard deviation by the mean of the observed ones.
CI_MODE_AVAILABLE - Static variable in interface org.metaqtl.IMetaQtlConstants
  SD Mode : use the available information to compute the standard deviation.
CI_MODE_LOD - Static variable in interface org.metaqtl.IMetaQtlConstants
  SD Mode : use only the confidence interval information if defined to compute the standard deviation.
CI_MODE_MAXIMAL - Static variable in interface org.metaqtl.IMetaQtlConstants
  SD Mode : compute the standard deviation using both lod support and rsquare information (if available) and then choose the maximal standard-deviation.
CI_MODE_RSQUARE - Static variable in interface org.metaqtl.IMetaQtlConstants
  SD Mode : use only the rsquare information if defined to compute the standard deviation.
CI_WIDTH - Static variable in class org.metaqtl.graph.QtlLayer
  The default width of the CI of the Qtl
ci_width - Variable in class org.metaqtl.graph.QtlShape
clog - Variable in class org.metaqtl.EMResult
  The complete loglikelihood.
ClustAlgorithm - Class in org.metaqtl.algo
ClustAlgorithm(IBioGenome, IBioOntology) - Constructor for class org.metaqtl.algo.ClustAlgorithm
ClustAlgorithm(IBioGenome, String, IBioOntology) - Constructor for class org.metaqtl.algo.ClustAlgorithm
cluster - Variable in class org.metaqtl.ChromCluster.ClusterGraph
clusterings - Variable in class org.metaqtl.MetaQtlResult
  The meta qtl clusterings.
clusters - Variable in class org.metaqtl.ChromCluster
  The list of the cluster members.
CMarkerSequence - Class in org.metaqtl
  A Common marker sequence between two ordered set of markers is a sub-set of at least two markers which order is the same between the two sets (may be reverse).
CMarkerSequence(int[][], int) - Constructor for class org.metaqtl.CMarkerSequence
  Initiates a new Common marker sequence from the tow arrays of common marker indices `mcidx[0..1][0..nmc-1]`.
CmdLineParser - Class in org.metaqtl.main
  Largely GNU-compatible command-line options parser.
CmdLineParser() - Constructor for class org.metaqtl.main.CmdLineParser
CmdLineParser.IllegalOptionValueException - Exception in org.metaqtl.main
  Thrown when an illegal or missing value is given by the user for an option that takes a value.
CmdLineParser.IllegalOptionValueException(CmdLineParser.Option, String) - Constructor for exception org.metaqtl.main.CmdLineParser.IllegalOptionValueException
CmdLineParser.NotFlagException - Exception in org.metaqtl.main
  Thrown when the parsed commandline contains multiple concatenated short options, such as -abcd, where one or more requires a value.
CmdLineParser.Option - Class in org.metaqtl.main
  Representation of a command-line option
CmdLineParser.Option.BooleanOption - Class in org.metaqtl.main
CmdLineParser.Option.BooleanOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.BooleanOption
CmdLineParser.Option.BooleanOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.BooleanOption
CmdLineParser.Option.DoubleOption - Class in org.metaqtl.main
  An option that expects a floating-point value
CmdLineParser.Option.DoubleOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.DoubleOption
CmdLineParser.Option.DoubleOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.DoubleOption
CmdLineParser.Option.IntegerOption - Class in org.metaqtl.main
  An option that expects an integer value
CmdLineParser.Option.IntegerOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.IntegerOption
CmdLineParser.Option.IntegerOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.IntegerOption
CmdLineParser.Option.LongOption - Class in org.metaqtl.main
  An option that expects a long integer value
CmdLineParser.Option.LongOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.LongOption
CmdLineParser.Option.LongOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.LongOption
CmdLineParser.Option.StringOption - Class in org.metaqtl.main
  An option that expects a string value
CmdLineParser.Option.StringOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.StringOption
CmdLineParser.Option.StringOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.StringOption
CmdLineParser.OptionException - Exception in org.metaqtl.main
  Base class for exceptions that may be thrown when options are parsed
CmdLineParser.UnknownOptionException - Exception in org.metaqtl.main
  Thrown when the parsed command-line contains an option that is not recognised.
CmdLineParser.UnknownSuboptionException - Exception in org.metaqtl.main
  Thrown when the parsed commandline contains multiple concatenated short options, such as -abcd, where one is unknown.
cms - Variable in class org.metaqtl.ChromCluster.ClusterEdge
CMSAlgorithm - Class in org.metaqtl.algo
  Use this class to find common marker sequences between two chromosomes.
CMSAlgorithm() - Constructor for class org.metaqtl.algo.CMSAlgorithm
COLLECTION - Static variable in interface org.thalia.bio.IBioEntityTypes
color2string(Color) - Static method in class org.metaqtl.graph.MetaGraphPar
COMMON_STROKE_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar
compare(Object, Object) - Method in class org.thalia.bio.util.BioEntityNameComparator
compare(Object, Object) - Method in class org.thalia.bio.util.LocusPositionComparator
computeCOV(double[], EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm
  Computes the variance-covariance matrix of the mixture component estimates.
computeCriteria() - Method in class org.metaqtl.EMResult
  This methos computes the following criteria : AIC AIC3 ICOMP MIR BIC AWE
computeDM(double[], double[], double[], EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm
  Computes the matrix of derivatives of the update function.
computeQtlSD(int) - Method in class org.metaqtl.Chromosome
  According to the given standard deviation computation mode this method computes for each QTL the value of the standard deviation of the QTL position.
ConsMap - Class in org.metaqtl.main
ConsMap() - Constructor for class org.metaqtl.main.ConsMap
copy(EMResult, EMResult) - Static method in class org.metaqtl.EMResult
cov - Variable in class org.metaqtl.MultiFitResult
  The variance-covariance matrix of the parameter estimates.
criteria - Variable in class org.metaqtl.EMResult
  The model choice criteria.
cross - Variable in class org.metaqtl.Qtl
  The QTL cross design.
CROSS_SIZE - Static variable in interface org.metaqtl.IBioGenomeProperties
  The cross size key.
CROSS_TYPE - Static variable in interface org.metaqtl.IBioGenomeProperties
  The cross type key.
crossLayers - Variable in class org.metaqtl.graph.MetaGraph
CrossPopulation - Class in org.thalia.bio.entity
  Class Description Here
CrossPopulation() - Constructor for class org.thalia.bio.entity.CrossPopulation
CrossPopulation(String, IBioEntity) - Constructor for class org.thalia.bio.entity.CrossPopulation
CrossPopulation(String, IBioEntity, int) - Constructor for class org.thalia.bio.entity.CrossPopulation
crossToString(int, int) - Static method in class org.thalia.bio.util.BioCrossTypes
cs - Variable in class org.metaqtl.Chromosome
  The size of the offspring population.
css - Variable in class org.metaqtl.CMarkerSequence
  The sizes of the common sequences
ct - Variable in class org.metaqtl.Chromosome
  The type of the offspring population.

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV LETTER NEXT LETTER | FRAMES NO FRAMES

A B C D E F G H I K L M N O P Q R S T U V W X Y Z